Dr Mohammad R.N. Avanaki

Supervision

Education
Current status: Post-doctoral fellow, Washington University in St. Louis (2011-Present).
Member of Optical Imaging Laboratory.
PhD: Medical Image Computing, University of Kent, United Kingdom (2008-2011).
Member of Neurosciences and Medical Image Computing (NMIC) group.
Member of Applied Optics Group (AOG).
MA: Postgraduate Certificate in Higher Education, University of Kent, United Kingdom (2009-2011).
MSc (Hons): Electrical Engineering, University of Semnan, Iran (2005-2007).
Member of Fibre Optic Sensor Design (FOSD) group.
BSc (Hons): Electrical Engineering, Isfahan University of Technology, Iran (2001-2005).

Professional

Awards and Honours
Co-author of Best Poster Award, Photonics West SPIE conference (2013).
Most Standardized Poster, Selected by the Writing Center of Washington University in St. Louis (2013).
Invited Speaker, International Conference on Radiology and Imaging, Chicago, USA (2013).
Awarded travelling grant by European Microscopy Society to attend Photonics West SPIE conference (2011).
Awarded bursary to attend the 8 th European Biophysics Congress, Hungary (2011).
Awarded travel grant to attend the 1st International Conference of Medical Physics, Iran (2011).
First Poster Prize Winner, Microscience Conference, London, UK (2010).
First Poster Prize, Centre for Biomedical Informatics (CBMI) Symposium, Kent, UK (2009).
Best Lecturer Award, Electronics Department of Azad University in Karaj, Iran (2008).
Outstanding Student, Electronics Department of University of Semnan, Iran (2007).
Best paper Presented in Student’s Ideas Congress, Tehran, Iran (2006).
Second Top Student, Electronics Department of Isfahan University of Technology (2004).
Selected in the Regional pre-college Mathematics Olympiad, Karaj, Iran (2001).

Research interest
Photoacoustic (PA) imaging.
Photoacoustic Computed Tomography (PACT).
Optical Resolution Photoacoustic Microscopy (OR-PAM).
Acoustic Resolution Photoacoustic Microscopy (AR-PAM).
Optical coherence tomography (OCT).
Dynamic Focus OCT (DF-OCT).
Spectral Domain OCT (SD-OCT).
Full Filed OCT (FF-OCT).
Confocal microscopy.
Aberration correction in confocal microscopy.
Medical signal / image processing.
Image enhancement and noise reduction algorithms.
Optical properties extraction from biomedical images.
Analysis the interaction of particles with light.
System specification improvement.
System resolution advancement.
Static and dynamic aberration correction.
Imaging Speed improvement.
Adaptive optics and aberration compensation.
Adaptive optics using spatial light modulator.
Adaptive optics using deformable mirror and wavefront sensor.
Sensor-less adaptive optics.
Focusing light within and through turbid media.
Resting-state functional connectivity in small animal and human brains.
Optimization.
Combined sequential algorithm.
Genetic algorithm.
Simulated annealing.
Particle swarm optimization.
Speckle noise reduction.
In-vivo / ex-vivo imaging.
Healthy and tumorous skin and lung tissues imaging.
Mouse brain functional and structural imaging.
Medical image compression.
Wavelet.
Fractal.
Hybrid techniques.
Professional Associations
Society of Photo-Optical Instrumentation Engineers (SPIE).
International Association of Engineers (IAENG).
European Microscopy Society (EMS).
International Congress for Global Science and Technology (ICGST).
Bonyad-Nokhbegan (Outstanding students committee in Iran).
Thesis titles
PhD: “Hardware Improvement and Image Enhancement in High Resolution Non-invasive Optical Imaging Systems”, under supervision of Dr. Ali Hojjatoleslami and Professor Adrian Podoleanu, University of Kent, United Kingdom (2012).
MSc: “Signal processing of interferometric fibre optic gyroscopes”, under supervision of Dr. Farzad Tavakkol, University of Semnan, Iran (2007).
BSc: “Design and development of a simple Optical Time Domain Reflectometer”, under supervision of Dr. Azardokht Mazaheri, Isfahan University of Technology, Iran (2005).
Research Experiences at Washington University in St. Louis
Develop a method to acquire high resolution resting-state functional connectivity maps for mouse brain using 512 full-ring photoacoustic computed tomography (PACT).
Image mouse brain (in-vivo and ex-vivo) using PACT.
Develop a technique to image the functional connectivity in the mouse brain in capillary level using MEMS Optical Resolution Photoacoustic Microscopy (MEMS-OR-PAM).
Develop a first three-dimensional resting-state functional connectivity map in the mouse brain using Acoustic-Resolution Photoacoustic Microscopy (AR-PAM).
Implement a wideband simultaneous phase-only spatial light modulator characterization in spectral domain.
Use photoacoustic imaging to detect Amyloid plaque in transgenic mice in-vivo with scalp and skull intact.
Work with different biological dyes for staining brain tissue for imaging.
Analysis of functional brain images using Singular Value Decomposition (SVD) and Independent Component Analysis (ICA) techniques.
Generate a mouse brain atlas for any specific depth from the sagittal view images of Paxinos histology atlas.
Research Experiences at University of Kent
Improve a Time Domain Optical Coherence Tomography (TD-OCT) with dynamic focus at 1300nm for skin imaging.
Improve the transverse resolution in a Spectral Domain OCT (SD-OCT) by correcting aberration.
Develop an application in Labview (using VIs and Math script) to correct the non-linearity of scanners in optical coherence tomography systems.
Investigation of morphological features of basal cell carcinoma (BCC) using dynamic focus optical coherence tomography.
Design different solid phantoms using epoxy-resin and microspheres to evaluate the performance of the optical coherence tomography system and to assess the accuracy of an optical properties extraction algorithm.
Design and implement a sensor-less aberration compensation technique in optical fiber systems using four optimization algorithms (random search, simulated annealing algorithm, genetic algorithm and particle swarm optimization).
Develop several methods for speckle reduction of optical coherence tomography images, using artificial neural network, wavelet, spatial compounding technique and modified median filter.
Design algorithms for attenuation compensation of optical coherence tomography skin images.
Implement an algorithm for skin layer detection of optical coherence tomography skin images.
Implement algorithms to enhance the image quality of OCT images using deconvolution of the point spread function (PSF) of the OCT system from the original OCT image. The PSF was estimated from an OCT image taken from a homogeneous dispersed gold-microsphere-phantom.
Research Experiences at University of Semnan
Develop several algorithms for signal processing of the Interferometric Fibre Optic Gyroscope (IFOG).
Develop image processing algorithms to track aerial objects.
Study the comparison between the signal processing of the closed-loop and open-loop IFOGs.
Investigate the limitation of image transmission in optical fibre links.
Develop algorithms based on wavelet and fractal for image compression.
Develop an optimization algorithm based on fuzzy logic to optimize the consumption of fuel in a car.
Research Experiences at Isfahan University of Technology
Design and implement several Microcontroller (Atmel 80C51 and AVR) based circuits.
Develop an algorithm for video quality measurements in optical fibre links based on artificial neural network.
Design circuits and develop algorithms to control DC, AC and step motors using microcontrollers.
Design a simple Optical Time Domain Reflectrometer (OTDR). Â
Control processes by programming the Industry Standard Architecture (ISA).
Design and implement full color dot-matrix display.
PhD project
OCT is a high resolution imaging modality analogous to ultrasound which can produce three-dimensional images from the microstructures within the skin. In this project I modified a dynamic focus OCT (DF-OCT) for skin imaging at 1300nm specifically. I studied the feasibility of differentiating healthy and Basal cell carcinoma areas on the skin using the DF-OCT. To increase the quality of the images I have added some modifications to the system and developed image enhancement algorithms. Some of the algorithms are as follows: speckle reduction using artificial neural network, image quality improvement based on deconvolution technique and using point spread function (PSF) of the system, aberration compensation using adaptive optics in combination with blind optimization algorithms such as simulated annealing, genetic algorithm and particle swarm optimization. Towards modeling of the skin, we extracted optical properties from the OCT image using some image processing algorithms and extended Huygens-Fresnel theorem.

Selected publications
M. R. N. Avanaki, A. Bradu, I. Trifanov, A.B.L. Ribeiro, A. Hojjat, and A. Podoleanu. “Algorithm for excitation optimization of Fabry–Pérot filters used in swept sources.” IEEE Photon. Technol. Lett 25: 472-475 (2013).
Yao J., Xia J., Maslov K.I., M. R. N. Avanaki, Tsytsarev V., Demchenko A.V., Wang L.V., “Noninvasive photoacoustic computed tomography of mouse brain metabolism in vivo”, NeuroImage, 64 (1) , pp. 257-266 (2013).
M. R. N. Avanaki, A. Podoleanu, J. B. Schofield, C. Jones, M. Sira, Y. Liu, and A. Hojjat. “Quantitative evaluation of scattering in OCT skin images using the extended Huygens–Fresnel theorem.” Applied optics 52, no. 8: 1574-1580, Editors Selected for Publication in Virtual Journal for Biomedical Optics (VJBO) (2013).
M. R. N. Avanaki, R. Cernat, P. J. Tadrous, T. Tatla, A. Podoleanu, and A. Hojjat, “Spatial compounding algorithm for speckle reduction of dynamic focus OCT images”, Photonics IEEE letter (2013).Â
M. R. N. Avanaki, J. Xia, H. Wan, A. Q. Bauer, J. P. Culver, and L. V. Wang,” High-resolution photoacoustic resting-state functional connectivity imaging of the mouse brain”, submitted to PNAS (2013).
M. R. N. Avanaki, V. Soleimani and R. Mazrae-Khoshki, “Comparative Assessment on the Performance of Open-Loop and Closed-Loop IFOGs,” Optics and Photonics Journal, Vol. 2 No. 1, pp. 17-29 (2012).
M. R. N. Avanaki, M. Sira, S. A. Hojjat, A. Aber, J. B. Schofield, C. Jones, and A. G. Podoleanu, “Improved imaging of basal cell carcinoma using dynamic focus optical coherence tomography,” J. Invest. Dermatol. 131, S38 (2011).
M. R. N. Avanaki, A. Hojjat and A. Gh. Podoleanu, “Investigation of computer-based skin cancer detection using optical coherence tomography”, Modern Optics Journal, vol.56, Issue 13, pp. 1536 – 1544 (2009).
Awards and Honors
Co-author of Best Poster Award, Photonics West SPIE conference (2013).
Most Standardized Poster, Selected by the Writing Center of Washington University in St. Louis (2013).
Invited Speaker, International Conference on Radiology and Imaging, Chicago, USA (2013).
Awarded travelling grant by European Microscopy Society to attend Photonics West SPIE conference (2011).
Awarded bursary to attend the 8 th European Biophysics Congress, Hungary (2011).
Awarded travel grant to attend the 1st International Conference of Medical Physics, Iran (2011).
First Poster Prize Winner, Microscience Conference, London, UK (2010).
First Poster Prize, Centre for Biomedical Informatics (CBMI) Symposium, Kent, UK (2009).
Best Lecturer Award, Electronics Department of Azad University in Karaj, Iran (2008).
Outstanding Student, Electronics Department of University of Semnan, Iran (2007).
Best paper Presented in Student’s Ideas Congress, Tehran, Iran (2006).
Second Top Student, Electronics Department of Isfahan University of Technology (2004).
Selected in the Regional pre-college Mathematics Olympiad, Karaj, Iran (2001).
Achievements in Sport
Gold medal in British Colleges and Universities Championship (BUCS), Kumite, Sheffield, UK (2012).
Awarded 4th Dan balck belt (2012) from Kan-Zen Ryue Federation.
International karate refreree certificate level C, Miami, USA (2012).
3×Gold in M.A.A.S.I.F open championship, Canterbury, UK (2011).
Bronze medal in International Karate Championship, Kumite 3th place, London, UK (2010).Â
Gold medal in M.A.A.S.I.F summer open championship, London, UK (2010).
Silver medal in Karate Shinboku Kai’s Art of Movement Annual Kata and Kobudo International Tournament, senior Kata 2nd place, London, UK (2010).
Sports man of the University of Kent (2010).
Top rate sport scholarship for Karate sport from University of Kent Sports Center in 2009 and 2010.
Gold medal in British Colleges and Universities Championship (BUCS), senior category (-67kg), individual Kumite, Sheffield, UK (2009).
Bronze medal in European Universities Karate Championship, European University Sports Association (EUSA), Spain, (2009).